The more we know the more we notice.

Archive for January, 2011

John Davison has many interesting things to say about the recognition that evolution is over. Here are two from his essay, An Evolutionary Manifesto (not to be confused with “ ‘the’ Evolutionary Manifesto”, an entirely different, and later, document). Davison writes:

In 1942, Julian Huxley wrote Evolution: The Modern Synthesis in which he summarized a consensus among certain geneticists, systematists, and paleontologists that evolution was a Darwinian phenomenon, guided by chance and natural selection… Perhaps the most remarkable feature of the text is the revealing and totally contradictory summary that Huxley offers on page 571, seven pages from the end.

“Evolution is thus seen as a series of blind alleys. Some are extremely short — those leading to new genera and species that either remain stable or become extinct. Others are longer — the lines of adaptive isolation within a group such as a class or subclass, which run for tens of millions of years before coming up against their terminal blank wall. Others are still longer — the links that in the past led to the development of the major phyla and their highest representatives; their course is to be reckoned not in tens but in hundreds of millions of years. But all in the long run have terminated blindly. That of the echinoderms, for instance, reached its climax before the end of the Mesozoic [before 65 million years ago]. For arthropods, represented by their highest group, the insects, the full stop seems to have come in the early Cenozoic. [Early Cenozoic means Paleocene, between 65 and 56 million years ago.] Even the ants and bees have made no advance since the Oligocene. [The Oligocene is part of the Cenozoic, 56-34 million years ago.] For the birds, the Miocene [23 to 5.3 million years ago] marked the end; for the mammals the Pliocene [5.3-2.6 million years ago, or so].”

Darwin famously ended his Origin of Species with these words:

…from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

But here is Huxley, Darwin’s admirer, admitting nearly 80 years ago, that the evidence is against ongoing evolution.

Davison continues his argument, quoting paleontologist Robert Broom who wrote a book called Finding the Missing Link, (1951) in which, on page 107, he had this to say about the Eocene, a geologic period now assigned to the time between 34 and 56 million years ago:

In Eocene times — say between 50,000,000 and 30,000,000 years ago — small primitive mammals rather suddenly gave rise to over a dozen very different Orders — hoofed animals, odd-toed and even-toed, elephants, carnivores, whales, rodents, bats and monkeys. And after this there were no more Orders of mammals ever evolved. There were great varieties of evolution in the Orders that had appeared, but strangely enough Nature seemed incapable of forming any more new Orders. What is equally remarkable, no new types of birds appear to have evolved in the last 30,000,000 years. And most remarkable of all, no new family of plants appears to have evolved since the Eocene. All major evolution has apparently come to an end. No new types of fishes, no groups of molluscs, or worms or starfishes, no new groups even of insects, appear to have been evolved in these latter 30,000,000 years.

New species of mammals continued to be produced for a while, ending with some primate types and finally ourselves.

OK, this is where the problem lies: in order to have genuine evolution — producing new species, new genera, new families, new orders, classes, and phyla — you must have chromosomal reorganization. That, however, is something that takes place in an individual cell, not in a population. So now, suppose you have a cell that is ready to start a new species — where is it? Where is its mom? And where is her mate?

Suppose her mom is a dinosaur. She is ready to be a bird. How did that happen? If the cell change happened in her mom’s germ plasm, where did her mom find a dad whose germ plasm could match up? It had to happen — the very same quirky, extraordinary, once-in-a million-years change that reorganized dino germ plasm into bird pattern — had to happen in her mom and her dad both at once. That is just unreasonable. It’s magic. It’s not a miracle, because it’s really of no spiritual significance, but it’s not an accident either. A scientist has to look farther, because how could it happen that way?

We’re stuck. No chromosomal reorganization: no evolution. Chromosomal reorganization: no mate. Simultaneous chromosomal reorganization in two individuals in the same locale, at the same time, and they meet and mate although there is no outward indication of the compatibility of their germ plasm: not reasonable.

The mom has to reproduce without a dad, and that is the only solution. It’s called asexual reproduction in the lower animals, and parthenogenesis (which is Greek for virgin birth) in the higher animals. It’s rare (in the higher animals) but there are enough examples around so we can study the process and think about it. Anyway, species generation is also rare, so we don’t want a common process. If we take this route, the mother with a change in her germ plasm can have several offspring with different genes but the same rearrangement of her germ plasm, so they are not identical twins, but they are the same new species: they can mate.

If you remember enough genetics, you will quickly object that all her offspring must for sure lack the “y” chromosome, and must therefore be sisters. End of story.

Not quite. Fact is, the “x” chromosome has all the genetic information needed to make the male; it’s not easy or obvious, but it is possible. The “y” chromosome is about preventing certain aspects of the “x” so development goes in the “y” direction. Since this is a blog, not a book, and I’m not the zoologist, I can promise only a little more detail, later. I refer you to John Davison’s essay, “An Evolutionary Manifesto” for more detail. Do not make the mistake of looking at “‘the‘ evolutionary manifesto” which is a completely different document on a different topic.

What Davison says in his paper is that there have been various experiments with parthenogenesis, and indeed the offspring are mostly female, but with a few males. One is enough, of course.

If asexual reproduction is the correct paradigm — and it has no competition — then we are fully and finally rejecting sex as the means of evolution. In fact, looking more closely, we are saying that increasing commitment to sexual reproduction is lethal to evolution. What a surprise! Microevolution, which is just about varieties and not about species at all, is sexual in its nature. Macroevolution, on the other hand, is asexual. The whole business of seeking the engine of evolution in sexual reproduction, natural as it seemed to Darwin and all his farming, variety-producing, cultivar cultivating contemporaries, is a blind alley. You need a 180. No sex.

Darwin himself was certain that evolution must proceed the same way that the development of cultivars or animal varieties takes place on a farm – inch by inch, each generation producing offspring just barely different from the previous, until the desired improvements are achieved and then locked in place by the wise farmer. Remember also, that he wrote almost 100 years before Watson, Crick, and Rosalind Franklin. He really had no idea even of the cell, let alone the chromosomes or the intricate strand of DNA, so that Behe has written a book, Darwin’s Black Box, titled on that ignorance and its consequences for Darwin’s theory.

The principal evidence that Darwin hoped would verify his theory was expected to be found in the geologic column. The discovery of the long-term fossil sequence was still fairly new in his day; William Smith had already (50 years before) mapped the underside of England and found distinct coal deposits with different fossils; but the changes from one species to another were abrupt, not gradual. This Darwin attributed to the incompleteness of the fossil record, and he was sure it would be remedied over time.

Well, it was not. The sequence remains the same (or similar) everywhere, and so the evidence for a long history of successive life forms is not in doubt, but no full set of minute transitions from one species to a daughter species has yet turned up.

Meantime, almost immediately after Darwin published Origin of Species, Mendel published papers on inheritance that showed its stability and that it was based on specific inheritance factors. When you cross a tall-vined and a short-vined pea plant, you don’t get a medium-height vine; you get some tall and some short. This was a surprise. Darwin was imagining a mushier inheritance, where everything runs together and changes by imperceptible degrees, like a slow change in ocean temperature. For a long time, Mendel’s disturbing paper was just ignored.

In the end, after 40 years of “forgetfulness,” Mendel’s work was resurrected, however, and the neo-Darwinians faced that inheritance is based on little discrete elements, on specific pieces. The new theory located Darwin’s gradual changes in these little pieces (called genes) and taught random variation in the genes. Neo-Darwinism is thus the incorporation of genes into the Darwinian theory.

But single genes still don’t make a species-change, and the geologic record still doesn’t have the imperceptibly gradual changes that Darwin expected and on which he staked his theory. Gene by gene (or at least very gradual) changes are there, but they don’t lead to new species; new species are there, but they arrive quite suddenly. Eventually, Darwinists (still keeping his name) had to content themselves with facing long periods of no evolutionary activity, punctuated by sudden, species-producing jumps. They called this saltation or “punctuated evolution,” which is an oxymoron because it isn’t evolution (gradual change) when nothing is happening, and it isn’t evolution when something dramatic suddenly happens, either.

Darwinism vs point mutations

the random accumulation of “point mutations” – that is, individual single mutations at particular points in the strands of DNA that make up an animal’s genome and

the competitive establishment of these new genes which make small changes in body proteins and consequently in body functions. Some of these changed functions help a body and give family members a competitive advantage. They have more or stronger offspring; they take over the world – or at least some niche of it.

All this may be abbreviated as: “random variation and survival of the fittest.”

One point, several points: same-same

A single point mutation does not make a new species, but, say the neo-Darwinists, a sufficient collection does. It is claimed that you need some separation between the old and the developing species so enough changes can collect to make a real difference.

As originally proposed, the theory is dead. Random point mutations do not change species because new species require chromosomal re-patterning. Without such a pattern change, various offspring can mate with fertility, and in that case, they are not a new species. A point mutation does not change the pattern, only one of its elements. A checkerboard is still a checkerboard when one set of squares is gray instead of black. If the second coloration drops out completely, however, then the pattern does change. Or if a third pattern element is superimposed, such as making every third square yellow, then also the pattern is changed and you can’t play checkers. In such a way, the change of a single gene does not make a new species, but a new chromosomal pattern does.

Now, point of logic, please:

If one gene does not change the species, how can two? One gene does not change the species, right? So after this change you have the same species and you change one gene, and that doesn’t change the species either. So if one change doesn’t change the species, then two don’t change the species, and neither do three or four…

Point mutations don’t change a species, not even lots of them accumulating.

Chromosomal re-patterning

One way that chromosomal re-patterning happens is that a whole section of the DNA strand is flipped around and re-attached upside down or in a different place on the strand, or even on a different strand. If (big “If” here!)… If the body pattern resulting from this re-attachment and re-patterning is viable, then it may also be a new species, which does not reproduce with its parent species but breeds true among its siblings.

Thus on my property, I have red maples and silver maples and box elders (ash-leaved maples) and they don’t cross with each other, though they are all maple trees. Apparently, they are real species.

On the other hand, I have had dogs that reproduced with other quite different dogs; in this case, we must be talking about different varieties, not different species, because they all reproduced very successfully.

Now, a glance at what is involved in simple cell division could make it seem a near-miracle (an incredibly unexpected event) that reproduction is ever successful at all. The strands are so delicate, the charges and chemistry so mind-bogglingly ephemeral, the little soup tureen (cell) in which all this must unfold (and re-fold) so crowded! From that point of view, neither a point mutation nor a re-patterning is all that surprising. It makes sense that not every such point mutation would be attractive or helpful to a species, and not every re-patterning would offer a new and viable body plan. But that such changes would arise is fully to be expected.

Darwinism has, more or less, (more among the researchers, less in the textbooks) accommodated these facts. Point mutation is not enough, if only because evolution proceeds in jumps, (saltation) which is what you would expect from chromosomal re-patterning.

If you’re thinking you have no idea what you’d “expect,” from re-patterning think of the set of chromosomes as a blueprint. If you change a room color, same house. If you lift a window from the blueprint and move it over a few feet, the house still won’t change unless you’ve put the window where the support beams go; then the house will collapse; not a viable house plan. If you take the car port and put it in the attic, you have a new pattern, and not a viable one. Change roof for floor: not viable.

Leave the kitchen as is and string out the rest of the rooms in a long row – now it’s a motel, not a house. It’s a new pattern and a viable building plan, but the pattern has changed so it’s not a family home: it’s a new species of building.

So there is a big difference between point mutations, even lots of them, and chromosomal re-patterning, even just once. Point mutations are a relic of old Darwinism and they just don’t square with either logic or the geological record as a way to produce new species. Chromosomal re-patterning could work, and work naturally.

Origin of species — a miracle?

With a clear definition of miracle in hand, we are in a position to ask whether the origin of species is a miracle. Certainly new species are amazing, and if, by new species, we meant only mankind, this origin might arguably be considered an event of religious significance. After all, we’re the ones who worship God.

The problem is that the origins of all new species of plants and animals, the millions of origins of plankton, kelp, buttercups, pink tarantulas, dung beetles, squirrels, and orangutans, have no clear religious significance. When a creationist attributes all new species to the direct hand of God, he is really calling all these events miraculous, even though they have no particular religious significance at all.

Meantime, the vocation of the natural scientist – his calling – is to find the natural causes of natural events. Once the geologic column has come into view so that we see how living forms have appeared in a slow succession and belong to deep history, we see that the origin of species is certainly not a single event, nor a series of events belonging to a single week. Thus, while an “omnipotent” God certainly has the “power” to complete any number of miracles in any succession he chooses, the miraculous origin of species over billions of years has a very different feel to it. Repeated miraculous intervention in the natural world, for a non-religious purpose, does not fit the definition of miracle, and it is reasonable to ask whether such a concept does not, in fact, cast doubt upon the vocation of the natural scientist. Is the natural event of species-origin one whose cause he ought not seek? That would be the logical conclusion of the creationist position.

To many, this seems an unreasonable conclusion, and the alternative line of reasoning – that species-origin is a natural event for which scientists should seek a natural cause — makes many religious people take evolution seriously. That Darwin said irreligious things does not close the case against his ideas; he could still be right. That there are gaps in the argument for evolution does not close the case; new ideas always need refinement.

What then?

Two problems:

From outside the sciences, there are two problems with Darwinism, or rather, two realms of difficulty: one philosophical, and one political.

The philosophical problem is that Darwinism, straight up, implies a denial of human nature. If we are no more than a gradual refinement of some simian cousin, then it follows, logically, that the transitional creatures between us and that simian were of uncertain humanity – and from that it follows, as a point of logic, that some of us might even now be more human than others; indeed some “humans” might not really be human, whatever that is.

The political problem flows quickly from the philosophical: precisely such a doubt about the universal dignity of the human person stood squarely behind the Third Reich. It stands behind the issue of abortion. It stands behind the developing issue of euthanasia. A brief glance at history suggests that further categories of dubious personal nature could be imagined and acted upon.

These philosophical and political problems are the reason why creationists hold firmly to the same miraculous concept of origin of species that was naturally held before geology presented the innumerable quirky species of the biosphere as a work in slow motion, even perhaps as a work still in progress. Although the concept of miracle is mightily stretched by invoking creation at the origin of each new species, and though the vocation of the biologist is mysteriously contracted, the creationist will have his human nature, whatever it takes. He firmly believes that his own religious nature suffices to spread the mantle of religious purpose over all species origin.

A Third difficulty

But there is a third realm of difficulty with Darwinism: the scientific realm. There are many natural reasons to doubt its sufficiency as a theory. Is it possible that if the scientific problems were addressed, there might arise a solution that did not suggest a denial of human nature?

Defining a miracle

Can we give a definition of “miracle” that is really tight, clear, and useful?

Sometimes, people offer definitions that simply mean anything astonishing or awesome. A big rainbow or a beautiful child is thus called a miracle. But, lovely as they are, rainbows and children are part of the normal course of nature; these may be miracles by analogy, but the word certainly means something that points to the divine in an unusual way.

So people may add the qualifier that a miraculous event must have religious significance; thus visions are called miracles. But again, visions can appear in the natural course of events, sometimes even in an unhealthy course of events; so this is not a good enough refinement. People think miracles are “good” through and through. It’s more.

One might say then, that a miracle is awesome, religious, and beyond normal possibility, so while the rainbow and the child are merely awesome, and visions problematic, a sudden remission from cancer qualifies as a miracle if you were praying for it.

But this is surely untidy. Sudden remission of a disease whose cause is unclear, and from which unexplained remissions are not infrequent, cannot be used to make a clear and persuasive definition. You can always thank God for such speedy remissions, and also for slow ones, but miracles, if they exist, are clear and stark — almost impossible — events.

Many then add that a miracle goes against the laws of nature, whereupon the atheists rumble that “Why would a god [no caps here] make laws and then break them?” or, indeed, “What laws?”

Laws of nature

First off, the laws of nature are not moral laws. God can break them if he wants to; He’s in charge.

More to the point: indeed, what are the laws of nature? Do we really know any? I mean, unexpected things are always happening; who can know what is possible? Today, there is no explanation; tomorrow there may be a perfectly simple one. It happens all the time in the sciences as well as in every other human endeavor. All the time.

What laws?

There is, however, an interesting law of physics which has been accepted “as law” for over a hundred fifty years now: the law of entropy, which states that, while matter and energy are completely conserved, their orderliness, which allows them to do work, always diminishes over time. This is called an increase in entropy – in mess if you will, in chaos; it is the universe running down. It is a law of probability and there is no escape.

A minor squabble with the biologists has arisen because biological systems seem to increase the local level of order, pulling all sorts of material into ever-larger coherent systems, impressing local energies to work on projects that come from within each bio-system. Are they bucking entropy as they enlarge their systemic constructions?

On the other hand, biological systems consume buckets of energy, spewing and scattering their heat back into the cosmos in total disarray. Thus the larger systems in the biosphere are costly; they are probably gaining entropy after all. In any case, if entropy is stopping or even being slowed by life, nobody has yet been able to measure it for sure.

A miracle is

It is in view of the law of increasing entropy that I would like to offer a definition of miracle that seems clear to me:

A miracle is 1) an awe-inspiring event, which is 2) of obvious religions significance, and which 3) involves a sudden and/or long-term remission of entropy.

Now, the interesting point here is that, yes, entropy is a physical law, but it is actually a statistical concept. Any small particular universe event is, physically considered, simply more or less likely, not absolutely posssible or not. Sometimes unlikely things happen, and if you were praying for them, you owe God thanks even if it isn’t absolutely awesome.

But the signature miracle, the beautiful word to the modern Thomas, is surely either the tilma of Guadalupe or the image of Las Lajas. In both cases, a religious image appeared quite suddenly, without paint or painter, and with a depth that defies all probabilities. The events are awesome; the images are obviously religious; and entropy stands completely challenged. Yes, a single an agave fiber might have been pressed into iridescence once or twice as houseflies are every day, but an entire tilma, no, and it wouldn’t have lasted more than 20 years anyway. The tilma of Guadalupe is from 1531, many times 20 years.

And yes, such or any such colorful grains of sand might be found in Ipiales or somewhere in the Andes of Columbia, and various vague figures can be imagined in many sedimentary rocks whose tumultuous history spills out endless, intriguing forms; but none of these constitute an entire assembly of friendly human (and religious) figures colored two feet deep into the rock.

These are miracles. They are not only records of miracles (they are that) but they are ongoing and have been left within our reach, giving us a contemporary clue as to the correct understanding of the miracles of scripture and history.

We believe that the Andes Mountains are 25 -30 million years old, or at least that is their start date, based on a variety of dating techniques. They took a long time to rise. But for a while, they were believed to be much younger, perhaps 7-8 million years old. The younger date is interesting because it provides a study in how easy it is to draw a mistaken conclusion from data that are good, but don’t quite cover all the bases.

The younger year date was based on the steep rise in the near-pure 16O in the sediments east of the Andes or in lake-bottom sediments in the area. Since such sediments come from the mountains, they represent chemical processes on the mountaintops; and since the proportion of 16O remaining in a cloud is greater the higher the cloud rises before dropping all its rain, the sudden increase in 16O sediments seemed to suggest a sudden rise in the mountains, — 4,000 feet in 4 million years.

This was not an unreasonable inference, though it was an awfully fast uplift.

However, in due time, someone pointed out that a simple increase in rainfall will pull the 18O out of a cloud leaving a higher proportion of 16O, and thus an increase in rainfall can change the isotopes available on the mountaintop just the same way as an increase in height. Was there an increase in rainfall during the rise of the Andes?

There was, and they did not spurt up in 4 million years, but took perhaps four times that long. All this just to say that there’s always a new twist, always something new to learn, always an unexpected turn of events in the sciences. You really want several converging lines of argument, not just one, no matter how carefully researched.

On the other hand, none of these events could have prepared anyone for the image of our Lady in the rocks of Las Lajas, at the back of a cave near Ipiales Columbia. And this brings me to an entirely different topic, a topic that is not specially related to any particular science, but to the philosophy of science. It is a topic that I would like to explore with this minor discussion of the Andes Mountains, the miraculous image they house, and the possibility of scientific error and correction all in the background.